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- PDB-4zlc: Crystal structure of the ROQ domain of human Roquin-2 -

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Basic information

Entry
Database: PDB / ID: 4zlc
TitleCrystal structure of the ROQ domain of human Roquin-2
ComponentsRoquin-2
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


regulation of miRNA metabolic process / negative regulation of T-helper 17 cell differentiation / T follicular helper cell differentiation / limb development / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / lung alveolus development / T cell homeostasis / B cell homeostasis / lymph node development / T cell proliferation ...regulation of miRNA metabolic process / negative regulation of T-helper 17 cell differentiation / T follicular helper cell differentiation / limb development / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / lung alveolus development / T cell homeostasis / B cell homeostasis / lymph node development / T cell proliferation / spleen development / post-embryonic development / P-body / positive regulation of non-canonical NF-kappaB signal transduction / RING-type E3 ubiquitin transferase / multicellular organism growth / RNA stem-loop binding / protein polyubiquitination / cytoplasmic stress granule / ubiquitin protein ligase activity / double-stranded RNA binding / T cell receptor signaling pathway / ubiquitin-dependent protein catabolic process / intracellular membrane-bounded organelle / mRNA binding / cell surface / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Four Helix Bundle (Hemerythrin (Met), subunit A) - #1790 / Roquin II / : / : / Roquin II domain / Roquin 1/2-like, ROQ domain / zinc-RING finger domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger ...Four Helix Bundle (Hemerythrin (Met), subunit A) - #1790 / Roquin II / : / : / Roquin II domain / Roquin 1/2-like, ROQ domain / zinc-RING finger domain / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Four Helix Bundle (Hemerythrin (Met), subunit A) / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsSakurai, S. / Ohto, U. / Shimizu, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science KAKENHI26711002 Japan
Japan Society for the Promotion of Science KAKENHI25291010 Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of human Roquin-2 and its complex with constitutive-decay element RNA
Authors: Sakurai, S. / Ohto, U. / Shimizu, T.
History
DepositionMay 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Roquin-2
B: Roquin-2
C: Roquin-2
D: Roquin-2


Theoretical massNumber of molelcules
Total (without water)70,3734
Polymers70,3734
Non-polymers00
Water73941
1
A: Roquin-2


Theoretical massNumber of molelcules
Total (without water)17,5931
Polymers17,5931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Roquin-2


Theoretical massNumber of molelcules
Total (without water)17,5931
Polymers17,5931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Roquin-2


Theoretical massNumber of molelcules
Total (without water)17,5931
Polymers17,5931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Roquin-2


Theoretical massNumber of molelcules
Total (without water)17,5931
Polymers17,5931
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.760, 60.868, 169.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROPROPROAA173 - 3243 - 154
21PROPROPROPROBB173 - 3243 - 154
12SERSERGLNGLNAA177 - 3227 - 152
22SERSERGLNGLNCC177 - 3227 - 152
13GLNGLNLYSLYSAA171 - 3201 - 150
23GLNGLNLYSLYSDD171 - 3201 - 150
14SERSERGLNGLNBB177 - 3227 - 152
24SERSERGLNGLNCC177 - 3227 - 152
15PROPROLYSLYSBB173 - 3203 - 150
25PROPROLYSLYSDD173 - 3203 - 150
16SERSERLYSLYSCC177 - 3207 - 150
26SERSERLYSLYSDD177 - 3207 - 150

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Roquin-2 / Membrane-associated nucleic acid-binding protein / RING finger and CCCH-type zinc finger domain- ...Membrane-associated nucleic acid-binding protein / RING finger and CCCH-type zinc finger domain-containing protein 2 / RING finger protein 164


Mass: 17593.250 Da / Num. of mol.: 4 / Fragment: UNP residues 171-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RC3H2, MNAB, RNF164 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9HBD1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 15% PEG6000, 100 mM Hepes, 100 mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 17819 / % possible obs: 99.1 % / Redundancy: 12.3 % / Rsym value: 0.169 / Net I/σ(I): 14.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementResolution: 2.7→49.438 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.916 / SU B: 31.751 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26009 910 5.1 %RANDOM
Rwork0.2241 ---
obs0.22596 16909 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.336 Å2
Baniso -1Baniso -2Baniso -3
1-5.37 Å2-0 Å20 Å2
2---4.86 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.438 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4748 0 0 41 4789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194833
X-RAY DIFFRACTIONr_bond_other_d0.0060.024721
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9676522
X-RAY DIFFRACTIONr_angle_other_deg1.35310822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.62723.548217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29815874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.291540
X-RAY DIFFRACTIONr_chiral_restr0.0860.2737
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025434
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021114
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5572.8552420
X-RAY DIFFRACTIONr_mcbond_other1.5582.8552419
X-RAY DIFFRACTIONr_mcangle_it2.534.2773018
X-RAY DIFFRACTIONr_mcangle_other2.534.2783019
X-RAY DIFFRACTIONr_scbond_it1.8473.0772413
X-RAY DIFFRACTIONr_scbond_other1.8463.0772414
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0474.5393505
X-RAY DIFFRACTIONr_long_range_B_refined4.61222.5195456
X-RAY DIFFRACTIONr_long_range_B_other4.61122.525455
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A92830.09
12B92830.09
21A81970.11
22C81970.11
31A85530.11
32D85530.11
41B83330.1
42C83330.1
51B85990.11
52D85990.11
61C79930.11
62D79930.11
LS refinement shellResolution: 2.699→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 75 -
Rwork0.302 1184 -
obs--94.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7755-0.4333-0.61181.79370.47992.910.13760.017-0.03110.0682-0.1125-0.267-0.00230.0242-0.02510.0539-0.0314-0.05070.06870.0860.27250.95771.4514-0.2834
20.37550.02860.31531.94740.19922.21490.15850.01210.00060.0792-0.0809-0.1506-0.0887-0.0749-0.07760.09640.02410.0040.14210.08930.30650.8787-30.23231.747
32.5927-0.34-0.33241.3617-1.30132.49360.22210.43350.2002-0.2674-0.08380.2579-0.2065-0.184-0.13830.34550.1713-0.05190.14940.04760.1455-3.5609-25.8926-33.6307
42.4328-0.5824-0.19780.9224-0.94753.1849-0.0742-0.3386-0.11380.3210.0275-0.08190.23270.01620.04670.3471-0.0632-0.07690.08710.00840.0866-7.0779-2.105835.335
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A171 - 325
2X-RAY DIFFRACTION2B173 - 325
3X-RAY DIFFRACTION3C177 - 323
4X-RAY DIFFRACTION4D171 - 321

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